The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular data: Lupinus paynei from Simi Valley, California, and Lupinus excubitus from eastern California and the San Gabriel Mountains. Although some taxonomic conclusions can be extrapolated from this study, overall, these results warn against undersampling in phylogenetic studies of recently evolved groups.